MolNFT v1 · #124498 · protein

Crystal structure of hydf from thermosipho melanesiensis in complex with a [4FE-4S] cluster

5KH0 · Small GTP-binding protein: “Crystal structure of hydf from thermosipho melanesiensis in complex with a [4FE-4S] cluster”. X-ray diffraction, 1 ligand (SF4), 12 pockets (best druggability 0.68). MolNFT v1 #124498 on GenesisL1: 3D…

PDB: 5KH0
Type: protein
Length: 1,438 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Small GTP-binding protein
UniProt: A6LMQ7
Ligands: SF4
Pockets: 12 · best druggability 0.68

Structure

x-ray diffraction · 3 distinct chains · 39% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Small GTP-binding protein	protein	363	39% helix, 20% strand	A6LMQ7
B	Small GTP-binding protein	protein	363	39% helix, 20% strand	A6LMQ7
C, D	Small GTP-binding protein	protein	356	39% helix, 19% strand	A6LMQ7

Ligands and binding sites

SF4 · Iron/sulfur cluster · ligand · 4 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	213	0.68	0.86	37	empty
2	143	0.63	0.86	26	SF4
3	456	0.61	0.75	50	SF4
4	342	0.59	0.76	32	SF4
5	112	0.57	0.85	18	empty

Interfaces

6 interfaces between chains.

A–B · 1548 Å² buried · 27 hydrogen bonds · protein-protein
C–D · 1545 Å² buried · 26 hydrogen bonds · protein-protein
A–D · 406 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 334 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 258 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

5KH0 · Crystal Structure of HydF from thermosipho melanesiensis in complex with a [4Fe-4S]… · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt A6LMQ7
Elsewhere: RCSB PDB 5KH0 · PDBe 5KH0 · UniProt A6LMQ7

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